August 22, 2018

Assuming you haven’t been sleeping under a rock, you have probably heard that a Nature paper came out on an F1 Neanderthal-Denisovan hybrid. The major new science in my opinion from the results of the genome itself is to be found in the figure above. It confirms that there was a lot of population turnover among Neanderthals, as this individual’s mother is more closely related to European Neanderthals who flourished ~40,000 years later than conspecifics from the same region 30,000 years earlier. This is not surprising in light of what we know about the genetics and paleoecology of this group, though it confirms what we know and increases our confidence.

Rather, what is surprising is that this paper was published because they found an F1. From their conclusion:

It is notable that one direct offspring of a Neanderthal and a Denisovan (Denisova 11) and one modern human with a close Neanderthal relative (Oase 1) have been identified among the few individuals from whom DNA has been retrieved and who lived at the time of overlap of these groups…In conjunction with the presence of Neanderthal and Denisovan DNA in ancient and present-day people…this suggests that mixing among archaic and modern hominin groups may have been frequent when they met.

The number of ancient genomes from these species/groups/lineages is literally in the range a handful. And among the early finds is an F1! This seems highly unlikely. It could be a fluke. Or, as inferred above, F1’s may have been very common when different hominin lineages met.

But that makes one ask: how is it that Neanderthals and Denisovans remained some genetically distinct over hundreds of thousands of years? The two reasons offered are that the lineages were geographically very distant from each other on the whole, and, that hybrid individuals had very low fitness. I think the former is the primary dynamic to focus on.

…we estimate that maximum interbreeding rates between the two populations should have been smaller than 0.1%. We indeed show that the absence of Neanderthal mtDNA sequences in Europe is compatible with at most 120 admixture events between the two populations despite a likely cohabitation time of more than 12,000 y. This extremely low number strongly suggests an almost complete sterility between Neanderthal females and modern human males, implying that the two populations were probably distinct biological species.

And the second:

Recent studies have revealed that 2–3% of the genome of non-Africans might come from Neanderthals, suggesting a more complex scenario of modern human evolution than previously anticipated. In this paper, we use a model of admixture during a spatial expansion to study the hybridization of Neanderthals with modern humans during their spread out of Africa. We find that observed low levels of Neanderthal ancestry in Eurasians are compatible with a very low rate of interbreeding (<2%), potentially attributable to a very strong avoidance of interspecific matings, a low fitness of hybrids, or both.

Models are models, and they have assumptions. Don’t have the player, hate the model assumption and revisit your priors.

There are 22 ancient genomes from 40,000 years ago or before. One of them is an F1 between Neanderthals and Denisovans. And another, Oase 1, has a Neanderthal in their very recent ancestry. The sampling locations may not be totally representative. The Denisova cave is likely to be special because it’s at the nexus of the ranges of the two Eurasian archaic lineages. But with that out of the way, it seems very unlikely to me that very low fitness or very low likelihood of mating when it close contact is the reason that the lineages remained distinct. After less than half a dozen samples from Denisova, cave researchers hit on an F1. What are the chances?

And yet, if matings between the lineages occurred when they were in close contact, and they were genetically distinct nevertheless over such long periods, then that demands an explanation. Denisova hominins and Neanderthals were genetically closer than modern humans are to either. At the time that F1 was conceived the two lineages had been distinct for ~300,000 years. This is not qualitatively much longer than some modern human groups (e.g., Khoisan vs. everyone else) have been diverging. And yet, like the Denisovan-Neanderthal split, modern humans have a lot of population structure and evidence of isolation (also, note that modern humans show no evidence of reduced reproductive fitness from offspring and purification of admixture, as has been inferred for Neanderthal genomic regions in modern human genomes).

All this leads me to conclude that in Pleistocene hominins allopatry and metapopulation dynamics are the solutions to this quandary. The population density of archaic hominins was on average low, but you need to go beyond average. The distribution was possibly highly patchy and with large zones of little habitation. Gene flow across populations may have occurred, but they would run up to a wall of emptiness equivalent to the Atlantic ocean. Additionally, both Neanderthal and modern human ancient indicates a recurrent pattern of location population extinction and replacement. My hypothesis is that populations which were liminal to the range of both lineages, and so likely to have a higher load of admixture from the other lineage, were also in a marginal territory and most likely to go extinct and leave no descendants. Then, less admixed populations with larger numbers close to the core of the lineage range would repopulate the liminal region.

If the model is correct, I think the Altai was resettled by Neanderthals from the west after the Eemian interglacial.

A contrasting method to maintain genetic separation from allopatry (physical distance and barrier) are group cultural identities which maintain very strict endogamy. We see this over 2,000 years in India, where populations are co-localized but almost totally unrelated in any way you’d predict from geography. But 2,000 years is a blink of an eye geologically. The explanation for why Neanderthals and Denisovans, and various African human lineages, remained separate for hundreds of thousands of years as coherent populations despite some gene flow on the margins, has to be geology, geography and ecology. Domains where hundreds of thousands years of stasis on quite possible.

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February 22, 2018

The above tweet captures the essence of something that occasionally happens in science: a revelation that transforms our understanding of the possibilities of the real. 2010’s Neanderthal genome paper did that, transforming a field which was mostly skeptical or cautious of Neanderthal gene flow into modern lineages, to one that was accepting of the likelihood.

The team found flowstones covering parts of the artworks and scraped away samples for dating. In three caves, it turned out, some of the art was over 64,000 years old — about 20,000 years earlier than the first evidence of modern humans in Europe.

“They must have been made by Neanderthals,” said Dr. Pike.

Wil Roebroeks, an archaeologist at Leiden University who was not involved in the new study, said the evidence was conclusive. “This constitutes a major breakthrough in the field of human evolution studies,” he said. “Neanderthal authorship of some cave art is a fact.”

…

The colored, pierced shells themselves are probably not much older than that. Up until about 118,000 years ago, the cave was flooded, thanks to higher sea levels.

That finding provides strong evidence that the shells were made by Neanderthals. They were definitely living in Spain 115,000 years ago, while modern humans would not arrive in Europe for another 70,000 years.

The two new studies don’t just indicate that Neanderthals could make cave art and jewelry. They also establish that Neanderthals were making these things long before modern humans — a blow to the idea that they simply copied their cousins.

What to make of this? First, a shout out to my old friend John Hawks. He’s been slowly repairing the reputation of Neanderthals for many years, and now we’re almost there. Neanderthals had large brains. Their cranial capacities were the largest of all hominins. The idea that they were brutes without language, as Richard Klein hypothesizes in Dawn of Human Culture, seems ludicrous now.

Back in the early 2000s I read Stephen Oppenheimer’s The Real Eve, and one of the arguments that I thought was ludicrous at the time is that the dominance of African humans was not due to some distinct genetic advantage (as Richard Klein posited), but accumulated cultural capital which gradually but continuously compounded over time. Though one shouldn’t discount genes, especially in the context of gene-cultural coevolution, with hindsight it seems clear that a simple causal factor of genetic innovation driving advantages vis-a-vis Neanderthals may be too simplistic.

Papers such as Genomic insights into the origin of farming in the ancient Near East illustrate that first mover advantage can result in huge demographic consequences. Small groups of farmers in the hillocks of the Fertile Crescent 10,000 years ago transitioned to agriculture just early enough that their genetic impact on West and South Eurasian populations, as well as African ones, would be enormous. Similarly, the invention of the light chariot by the Sintasha people may have resulted in the spread of haplogroup R1a-Z93.

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November 21, 2017

We live in a time of transitions when it comes to Neanderthals. Since the 2010 discovery of strong genomic evidence for Neanderthal ancestry in most humans they’ve been…humanized. This was pretty much inevitable, but, I also think it was right. Neanderthals were a big-brained human species which dominated much of Eurasia for hundreds of thousands of years. Their culture did exhibit a certain stasis, but then so did that of our modern African ancestors ~200,000 years ago.

There has been a recent debate about how far back the divergence between Neanderthals and modern humans goes back. My own views is that it’s probably further back than 500,000 years, perhaps closer to 750,000 years, but that there may have been ancient gene flow between lineages as well.

A new paper is now out which suggests that Neanderthals persisted in southern Spain for 3,000 years after they disappeared elsewhere, Precise dating of the Middle-to-Upper Paleolithic transition in Murcia (Spain) supports late Neandertal persistence in Iberia. Obviously, I can’t evaluate the taphonomy and all that. There have long been debates by paleoanthropologists about this region and its Neanderthal habitation (some earlier dates suggested Neanderthals persisted down to 29,000 years ago in southern Spain, but those seem to be rejected). What I can say is that it is entirely expected that the Neanderthal range as it contracted would exhibit an s-shaped trajectory, with a tail where they persisted as relic populations in areas which they were particularly well adapted to.

As paleoanthropology and genetics progress I’m rather sure that we’ll drill-down on very detailed dynamics of interaction, and local succession and replacement. Though humans leave cultural artifacts behind, as a rule the first and last fossils in paleontology usually underestimate the time span that a species flourished. I wouldn’t be surprised if the same applied to Neanderthals, and some day someone with a suspiciously high Neanderthal ancestral fraction was sequenced or genotyped who lived just before the Last Glacial Maximum.

Also, I should mention for those of you looking for a pre-Christmas gift, my company’s Neanderthal product (which does a functional analysis of a set of characteristics where modern humans segregate ancestral and derived variants from the two lineages) can be had for $29.99, as Helix is discounting the $80.00 kit cost (the same applies to the $39.99 Metabolism product, though if you bought Neanderthal earlier then Metabolism is always$39.99 since Helix has banked your data).

People keep asking us the details of the Helix-Insitome relationship and how it works. So we decided to write a blog post addressing that (it’s very short), How does Helix work?.

P.S. we’re probably the only start-up in the world where regular office conversation occurs about Neanderthals.

June 30, 2017

The ancient genome from South Africa was of not because it confirmed what many had long suspected: the deep structure of modern humans in Africa goes back quite a bit further than we had been assuming. A few years ago I co-wrote an op-ed for USA Today where I initially wrote that the Khoisan divergence from other humans was around ~200,000 years ago. For various reasons I let a “fact-checker” change that to ~150,000 years ago. But as I told my co-author Alex Berezow people had access to whole genomes just leaning toward an older date than in the current literature.

Now we know that the date of divergence may be closer to ~300,000 years. Both because of the ancient DNA, and the Moroccan fossils which make it obvious that morphology associated with our own lineage was already beyond incipient before 300,000 years ago.

The past was more complicated than we think. Ancient DNA has made us toss many of our preconceptions out. For example, several years ago researchers concluded that the Out of Africa populations exhibited a different structure than we had thought. Populations of the Near East and Europe had ancestry from a group that was basal to all other non-Africans. That is, if you have a family tree then Oceanians, East Asians, Amerindians, Siberians, and European hunter-gatherers would be on one branch. On the other branch would be “Basal Eurasians” (BEu), named due to their basal position on the tree in comparison to all other non-Africans. Ancient DNA has not uncovered any population which is mostly BEu. Early Holocene Near Eastern populations, the various first farmers, invariably seem to show mixture between BEu and a West Eurasian element similar to what gave rise to the Mesolithic hunter-gatherers of Europe.

It seems possible we may never find “pure” BEu samples. We know that 10,000-15,000 years ago in Europe there was a massive expansion of a population of hunter-gatherers with stronger affinities to modern Middle Easterners than in the past. Perhaps this was part of a broader expansion of this group of hunter-gatherers across vast swaths of Western Eurasia, and in the process they absorbed the BEu populations until there were no pure populations left?

These questions were triggered by novel results which couldn’t be accommodated by current accepted models. This reminds me of a paper from over a year ago which presented some puzzling results which make much more sense now, Ancient gene flow from early modern humans into Eastern Neanderthals. The authors compared the Altai Neanderthal genome, the Denisovan genome, and those of modern humans (as well as a European Neanderthal). The stylized phylogenetic tree is one which the Neanderthal-Denisovan clade spits off from African proto-modern humans ~600,000 years ago. Then around ~400,000 years ago you see the divergence between Neanderthals and Denisovans. This gives us rough expectations as to the nature of the genetic variation in these populations, as they shared quite distinct periods of evolutionary history together and apart.

What the authors found is that a small minority of the Altai Neanderthal genome exhibited much stronger affinities to modern African populations than to the Denisovan. On the order of ~5%. Looking at the length of the haplotypes they estimated that the admixture occurred ~100,000 year ago. Curiously, at least at the time, this modern human population was basal to all modern humans. The authors estimate that the divergence from modern lineages occurred about ~200,000 year ago based on what was understood about modern human differentiation at the time.

At the time that was pushing it, though not unreasonably so. Now that number is probably comfortably defensible. One important point to note is that the modern human admixture was from a group equally related to all Africans. This implied that this group separated before the division of the Bantu and the Yoruba. So if you accept the most recent genomics then this group may date to closer to 260,000 years before the present. And in fact if the fossil record is correct they might have separated as early 350,000 years before the present. Additionally, the group which published the South African genome study posited another group, Basal Africans (BA), who diverged far earlier than the Khoisan from most African (and also non-African) groups.

Maximal Neanderthal range

The Neanderthals are a well studied group. We know what their range was. One can spit all sorts of speculative scenarios, from wide range proto-modern humans pushing deep in Eurasia during the Eemian interglacial 130,000 years ago. Or, it may have been through contact in the Near East and expansion of a somewhat admixed Neanderthal population north and east over time. Who knows? At least until there’s more ancient DNA….

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October 18, 2012

In antiquity what we term Tunisia and Tripolitania were part of “African province.” Just as “Asia” originally referred to the margins of what we now term Asia (regions of Anatolia), so “Africa” originally denoted a subset of the northwest fringe of the continent which became Africa. In biogeography this segment of the continent is actually not part of Africa (it is part of the Palearctic ecozone). And yet the vicissitudes of early modern cartography are such that continent had to be bounded by water on as many sides as possible, and today we clumsily make recourse to the term “Sub-Saharan Africa” to distinguish that region from the northern littoral, which is really part of the Mediterranean world.

July 19, 2011

So asks a commenter below in relation to the question above. First, why would one even presume that they were red-haired, see my 2007 post, or the paper in Science: A Melanocortin 1 Receptor Allele Suggests Varying Pigmentation Among Neanderthals. In humans loss of pigmentation can usually be thought of as loss of function on genes. That’s probably one reason that there are several different genetic architectures for light skin, but only one for very dark skin. There might be only one way for an engine to operate as designed, but there are many different ways you can tweak a part and render it broken.

The reason that scientists have posited that Neanderthals were red-haired is that they examined the region around a melanocortin receptor gene which serves as something of a master regulator in terms of melanin production. Their sample was of two Neanderthals, one from Italy and one from Spain, and both exhibited signs of loss of function within this region. An N = 2 is small, but one must recall the fact that they are independent draws as they were sampled from different regions. Also, since then from what I ...

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May 6, 2010

As a result, between 1pc [percent] and 4pc of the DNA of non-African people alive today is Neanderthal, according to the research. The discovery emerged from the first attempt to map the complete Neanderthal genetic code, or genome. It more or less settles a long-standing academic debate over interbreeding between separate branches of the human family tree. Evidence in the past has pointed both ways, for and against modern humans and Neanderthals mixing their genes.

…

Prof Svante Paabo, of the Institute for Evolutionary Anthropology in Leipzig, Germany, said: “Those of us who live outside Africa carry a little Neanderthal DNA in us.”

I will have a thorough write-up when I get a hold of the paper, which should be soon. As I said, this is a story of genomics, not just genetics. 1-4% is not trivial. The Daily Telegraph has more:

They were surprised to find that Neanderthals were more closely related to modern humans from outside Africa than to Africans.

Even more mysteriously, the relationship extended to people from eastern Asia and the western Pacific – even though no Neanderthal remains have been found outside Europe and western Asia.

The most likely explanation is that Neanderthals and Homo sapiens interbred before early modern humans struck out east, taking traces of Neanderthal with them in their genes.

Professor Svante Paabo, director of evolutionary genetics at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who led the international project, said: “Since we see this pattern in all people outside Africa, not just the region where Neanderthals existed, we speculate that this happened in some population of modern humans that then became the ancestors of all present-day non-Africans.

“The most plausible region is in the Middle East, where the first modern humans appeared before 100,000 years ago and where there were Neanderthals until at least 60,000 years ago.

“Modern humans that came out of Africa to colonise the rest of the world had to pass through that region.”

…

Several genes were discovered that differed between Neanderthals and Homo sapiens and may have played important roles in the evolution of modern humans.

They included genes involved in mental functions, metabolism, and development of the skull, collar bone and rib cage.

Image Credit: United Press International

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